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The ligand-free structure of human PPARgamma LBD Q286E mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6L8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 1.2 M Sodium citrate tribasic dihydrate, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.44 49.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.986 α = 90 b = 59.886 β = 103.399 c = 117.761 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2018-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.88 50 99.9 0.99 22.49 5.2 51089
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.91 0.75 1.96
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6L8B 1.88 49.818 50005 2592 98.234 0.189 0.1866 0.1946 0.2308 0.237 21.622
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.027 0.064 -0.075 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.644 r_dihedral_angle_4_deg 16.617 r_dihedral_angle_3_deg 13.068 r_dihedral_angle_1_deg 5.371 r_lrange_it 5.009 r_lrange_other 5.009 r_scangle_it 2.784 r_scangle_other 2.783 r_mcangle_it 2.063 r_mcangle_other 2.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.644 r_dihedral_angle_4_deg 16.617 r_dihedral_angle_3_deg 13.068 r_dihedral_angle_1_deg 5.371 r_lrange_it 5.009 r_lrange_other 5.009 r_scangle_it 2.784 r_scangle_other 2.783 r_mcangle_it 2.063 r_mcangle_other 2.063 r_scbond_it 1.681 r_scbond_other 1.68 r_angle_other_deg 1.278 r_mcbond_it 1.253 r_mcbond_other 1.25 r_angle_refined_deg 1.226 r_symmetry_nbd_refined 0.248 r_nbd_refined 0.204 r_symmetry_xyhbond_nbd_refined 0.186 r_nbd_other 0.185 r_symmetry_nbd_other 0.175 r_xyhbond_nbd_refined 0.163 r_nbtor_refined 0.155 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.067 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4257 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing